Memories
by CrystalCave
Summary: In which a new rune created by Clary sends Alec back in time to witness some of the many hardships in Magnus' life, all while trying his best not to mess up the future. Post COHF.
1. Chapter 1

Alec awoke to a kiss being pressed on his forehead. Last nights events suddenly came back to him, causing him to smile. Late night drinking, kisses, long conversation, and an overall lovely evening with his boyfriend, Magnus. Magnus' intoxicating sent of sandalwood caused Alec to open his eyes, and suddenly he was looking up at a messy haired, cat eyed, smirking warlock.

"Good morning, darling," Magnus mused.

"Mph," Alec groaned into his pillow, earning a chuckle from his lover above him.

"I hate to wake you up, but you're needed at the institute. Biscuit called me."

"Is everything okay?" Alec said, a look of concern on his face, searching Magnus' face for answers.

"Everything is fine, love. Biscuit has created a useful rune apparently, and all the shadowhunters are being asked to attend a meeting at 9:30. I just didn't want you to be late, I know how much you hate that." Magnus explained, soothing his boyfriend.

"Oh. Did she say what the rune was?"

"Wasn't really listening, your pulchritudinous sleeping figure was a little distracting." Magnus smirked, kissing Alec's cheek.

Alec forced himself out of bed, hopping into the shower and quickly shaving before making his way into the kitchen to brew himself some coffee. Alec was curious to find out why this new rune was so important that all the shadowhunters has to attend. He would much rather spend the day reading comic books with Magnus or entertaining Chairmen Meow. But being born half angel meant this was his job, and he wouldn't replace it for the world.

"I'm off, then," Alec said as he shrugged on his jacket. Magnus looked up from the spell book he was studying and smiled at his partner.

"Be careful, Alexander, I'll be waiting for you to arrive home."

Alec nodded at Magnus before heading out the door and walking towards the institute. The walk wasn't really that bad, and he had walked it possibly hundreds of times before he had come out.

"Alec," Jace exclaimed as Alec walked threw the institute doors. "You need to hear about this rune. Time travel. I can't believe it." Jace shook his head, leading his parabatai towards the meeting room.

The room was full of talking shawdowhunters, and all the conversations were about this new rune Clary was going to tell them about. Alec felt slightly uncomfortable, until he found Simon and Isabelle smiling at him

"Big brother!" Isabelle exclaimed.

"Hey, Iz. Jace said something about, uh, time travel? What does that even mean?"

"Time travel! Like, Back to the Future! Except, were not Doc and Marty in a DeLorean, although that would be sick. You should have seen-"

"Simon, shh. We don't know what you're talking about," Isabelle said, placing a finger on Simons lips, effectively making him be quiet.

"Well, whatever it is, it better be worth our time. The demon activity in New York this time of year is always high and having all the Nephilim in one place is rather ineffective." A voice behind Alec said. Turning around, he was greeted by none other than his father, the Inquisitor.

"Dad," Alec said, a little surprised, "Shouldn't you be in Idris?"

"I had to come for this rune. According to Ms. Fairchild, this rune could change everything. Even fix the mess that... Valentine created." Alec knew his Dad had a hard time talking about the man he used to practically worship so negatively. And while in made Alec frustrated and a little nauseous, he was able to put himself and his fathers shoes and understand. Their relationship had been improving since Robert had told Alec he was more of a man than he could ever be.

"Could it really? But, wouldn't that mess up the present time now? I mean, of course it would save people, but if it wasn't for the circle, and the Mortal and Dark Wars... everything would be different." Or he could possibly never meet Magnus. That was a thing too.

"I don't know, son. But it might be worth it." Robert sighed, turning his attention towards Clary and Jace, who were making their way to the front of the room.

The room got quiet, signaling Clary to talk, "I had a vision of... this rune. Its intention is to send you back in time to moments that you would like to have been there for, but couldn't be, because of circumstance or because of not being born yet. It's also supposed to be memories of the person you love the most, more than anyone. Memories that defined this person. That's all I know... obviously I haven't tried it..."

"I'll try it," Alec heard himself say before he even thought about it. Alec had always wanted to see the moments Magnus wrote about, and based on the rune Clary had made what seemed like lifetimes ago, Alec knew for sure the person he loved more than anyone was his Warlock.

"Alec, it could hurt you." Izzy said, "could it?"

"I don't know. I haven't really thought of how the person will come back from it."

"It's okay, Clary. I'm sure the rune will wear off eventually. I'll be happy to try the rune for us." Alec said, placing a friendly hand on Clary's shoulder.

"Thank you, Alec," Clary smiled, pulling out her stele. She drew the rune on Alec, and after a few seconds, Alec saw the world go black and suddenly he lost feeling in everything and, when he saw light again, he found himself in a place he never thought he would be. Batavia of the Dutch East Indies.


	2. Chapter 2

A few moments after appearing in what seemed to be way in the past, Alec realized that he must look ridiculously out of place. He swiftly activated his invisibility rune and just for safe measure, hid behind a nearby, run down barn.

"keluar di sini, anak! (Get out here, boy!)" He heard a deep voice yell viciously. He heard the slamming of a door, and then the nay of a few horses before he got the courage to look at the sight in front of him. And once he did, Alec could almost physically feel his heart rip in two.

Standing in front of him was boy, no older than twelve. He was dirty, matted hair gong slightly passed his shoulders. He was rail thin, wearing tattered clothes. His bright amber cat eyes stood in contrast to the rest of his dull, dirty appearance. With the combination of skin tone, bone structure, and of course his cat eyes, Alec clearly recognized this boy as his boyfriend back home.

Magnus was being dragged by his hair, flailing veraciously against his step fathers grip. Alec wasn't clear where they were going, and lost them for a minute before he heard a large splash. Eyes going wide, Alec ran as fast as his feet would take him, landing right next to the pond the boy was being forced in.

"Anda membunuh istri saya, setan! Mati! (You murdered my wife, demon! Die!)" The man grumbled, forcefully pushing his head into the water. It took all of Alec's will power to not run over and help. But he couldn't. That's not how it's supposed to happen.

Suddenly a large blue light appeared, followed by a scream. Alec lifted his head to see the evil man being burned to the ground. Alec knows how this effected Magnus for years to come. He knew how guilty this made Magnus, and how his step fathers cruel words effected him for hundreds of years after they were said.

Alec heard a small gasp. He rose his head to see the small boy, wide eyed, looking back and forth from his step dad to his hands. Magnus shook his hands a little bit, blue sparks falling out of them. Magnus' eyes had a mixture of wonder and terrified in them. He limped away from the pond and then ran towards the small house on a hill.

Alec felt a little creepy and invasive following him, considering for the first time, Alec was older than Magnus in this situation. Alec followed though, mostly based on curiosity, and because he needed to make sure Magnus would be safe.

Magnus walked passed the house to the backyard. Once there, he made his way to a headstone in the backyard, where Magnus seemed to collapse and lay down next to it. He put his head in his hands for a second before Alec heard the soft sobs that broke his heart.

Magnus was only a kid. Alec couldn't imagine dealing with the death of both your parents, and even more than that, thinking that it's all your fault, at such a young age. Alec could barely deal with being gay at his age. Alec obviously knew all about this, but reading about it was different than seeing it.

Suddenly, the vision went burry and then black, and before he knew it, he was staring up at a wide eyed Jace, Clary, and Isabelle.


	3. Chapter 3

**Hey guys! I *finally* learned how to write an authors note. I hope you all are enjoying this story so far! I've been consistently uploading once every other day. In order to write future chapters I'm going to have to reread The Bane Chronicles, so chapters might be a little delayed after this one. I have hella auditions and exams coming up, but I will try my best!**

 **Disclamer : it goes without be said that I don't own any character or concept in this story! All credits go to Cassandra Claire.**

"By the angel," Alec gasped when he first opened his eyes. He noted that he was now on his old bed, before he had moved to Magnus' loft. Around his bed was his parabatai, sister, and of course Clary, all looking down at him with concern, "What happened?"

"Once Clary put the rune on you, you just collapsed. Your heart stopped and it was like you were dead." Izzy said, gripping Alec's hand tightly.

"I felt our bond break, Alec. That was terrifying," Jace added, putting his palm over his parabatai rune, "But it just came back."

"What did you see? Was it about Magnus?" Clary said, almost seeming uncomfortable in the situation. Alec couldn't blame her, it must be a little odd being in the middle of such a tight sibling bond, especially because of the demon her brother turned out to be. Alec couldn't imagine living without his siblings by his side. He wasn't even sure if he would be living.

"I- uh- yeah, it was. Remember the story he told us at his party? About his mom? That's what I saw." That was all the detail Alec would go into. The details of Magnus killing his step father was most certainly not Alec's secret to tell.

"Oh, Alec I'm sorry. I can call Magnus if you want...?" Clary suggested, not wanting to interrogate the conversation any further.

"No, it's okay, Clary. I'll go see him right now. It's about lunch time anyways."

Alec made his was out of the institute and towards Magnus' loft. He wasn't sure what he was going to say once he saw him. While it's nothing he didn't know, it was still enlightening to see his boyfriend in this way. It made him feel closer somehow.

Alec wasn't even sure if he should tell Magnus what happened. What Magnus didn't know wouldn't hurt him. Plus, it might make Magnus uncomfortable. Naturally in relationships, you want to put your best self forward. So, it might make Magnus uneasy to know that Alec saw a moment that was so personal to Magnus. But, Magnus did say Alec was the first of so many things, so wouldn't him being the first to see his past be okay too?

Alec pulled himself out of his thoughts as he approached the loft door. He put the key Magnus had gave him into the lock and let himself in. He opened the door to find Magnus sitting on the ground, his hair all about the place, his cat eyes, wide and alert, looking at Alec with terror and sympathy.

"Hey, what happened to you, are you okay?" Alec asked curiously, closing the loft door and walking towards his partner.

"I'm fine but- oh lord, Alec, I'm so sorry," Magnus said softly, looking up at Alec with soft eyes.

"What for?"

"I don't really know what happened. One minute I was making a potion, and then the next I was in your childhood bedroom. I heard... what you dad said, Alexander. That wasn't okay-"

"It's okay, Magnus. My dad already apologized for being so closed minded in the past. I saw your past too, but it was because of Clary's rune." Alec said, point to the new rune on his wrist that Clary has drawn.

Magnus looked curiously, then looked down to see the same rune looking up at him from his wrist.


	4. Chapter 4

**A/N: I know Aldertree plays a completely different role in the books, but I decided to use the character of the TV show Aldertree tree as a bad guy in This fic. Raj also makes a appearance as well. Enjoy!**

"Magnus, what the hell?" Alec said, bewildered, "Does it hurt?"

"No I... I don't even feel it," Magnus said softly, looking up to meet Alec's eyes with a curious and concerned look on his face.

"But that doesn't make sense. If no one drew that rune on you, how is it there?"

"Lets go show Clary. She could help us," Magnus said, getting up to get his coat. Alec followed.

Magnus opened a portal, grabbing Alec by the hand and taking him with him. Alec could tell that this was scaring Magnus. The use of angelic runes on a warlock was very odd indeed.

When they arrived at the institute, they were met by a typical sight. Clary and Jace, of course, all over each other against a wall. Alec looked down at his hands while Magnus cleared his throat loudly, commenting, "It doesn't take you two long to get at it again."

"Magnus Bane," Jace smirked, turning his head towards the pair, "Seems a little hypocritical coming from you. I recall a certain hickey."

"Jace," Carly scolded, "Is everything alright, Magnus?"

"Of course, Biscuit, but it seems to be that your rune had an effect on me too," Magnus stated, showing his wrist to Clary.

"By the Angel, would you look at that," a voice behind them said curtly. The four of them looked over to see Aldertree, the current, annoying head of the New York institute give Magnus the death glare.

"I will have to report this to the clave. I don't know what spells you have done, downworlder, but no one here appreciates our runes on a... demon of sorts."

"Leave him alone. It isn't his fault." Alec said with a new found confidence, "It's because of Clary's new rune. She put it on me and, in turn, it went on Magnus as well."

"Looks like Clary might get in trouble too. I know your precious step father is also a downworlder but I wouldn't expect this from you, Clarissa." Aldertree said matter-of-factly, shaking his head in a disappointingly evil way.

This caught Jaces attention, "You won't touch Clary-"

"I can do whatever I please, Herondale, now if you don't mind I need Magnus Bane and Clary Fairchild to come to my office." Aldertree said curtly, making his way towards the door.

"I don't have to follow your rules, Nephilim. This is between Alexander, Carly and I. Now if you don't mind-"

"I would be happy to send a long, lengthy report to the inquisitor about their precious High Warlock of Brooklyn disrespecting my orders. And knowing your... relation to him, I don't know if he'd be to happy with it. Come with me, warlock." Aldertree said in a menacing fashion, opening the door.

Magnus and Clary shared a look before following Aldertree out, Magnus muttering, "who shit in your cereal..." making Clary giggle.

Once the trio had left, Jace and Alec made their way down to the main hall, where the met with some of their colleagues to discuss demon activity. Alec had almost forgotten about this whole situation until he heard a frightening familiar scream, coming from Aldertrees office.

"Magnus!" Alec proclaimed, running towards the noise. When he opened the door, the mix of worry and anger hit him like a truck.

Magnus was being held down by Raj, in a stiff wood chair. Clary was being held back for helping Magnus. And Aldertree was putting his stele right against the warlocks skin.


	5. Chapter 5

**A/N: I don't have an excuse! It's been too long. But good news is, I actually have a plan for this fic now! Hope you all enjoy!**

Alec's heart stopped but his fist didn't. He aggressively punched Aldertree directly in the nose, knocking him down long enough to carry Magnus' twitching body out of the awful office. "it's going to be okay Magnus... you're going to be okay..." he was saying to himself more than his boyfriend. Runes didn't work on warlocks, a proven fact. While they're claimed to be deadly, there hadn't been enough cases to be a fact. That was the only thing keeping Alec sane as he sprinted the first bedroom he saw.

Jace followed right behind Alec, calling out for any doctor he could find. Isabelle and Clary were not much farther behind, Izzy with a phone to her ear, calling Catarina and telling her the situation. Magnus groaned loudly, clutching hard at his wrist where the stele was placed.

Alec placed his love down on the bed with shaking hands and pulled over a chair and sat down next to him. He kissed Magnus' forehead as he went, holding back the tears behind his eyes the best he could. Never in his wildest dreams did he ever see Magnus being gone before he did. The thought made his stomach do flips and he quickly pushed it out of his mind. Magnus would be okay, he was sure of it. He had lived for hundreds of years. Surely a stele wouldn't kill him off just like that.

Just then, Catarina came bursting in the door. Her white hair was in a neat braid down the right side of her head and she was still in scrubs. The only thing that was out of the norm was the look of concern for her close friend laying on the bed.

"Hello Alec. What exactly happened?" Catarina said breathlessly, hurrying to her friends side. Her fingers were already bursting with magic before she had gotten to Magnus.

"Clary created a new rune, making us see some of each others memories. She put it on me but for some reason it showed up on Magnus as well.

It- the first one didn't hurt him. But uh, Aldertree held him down and the bastard tried to draw a rune on him. Is he okay?"

"I'm going to need you to leave the room. I'm sorry, Alec, but this magic is too powerful and it could hurt you. I'll get you as soon as I'm finished." Catarina said quickly, never taking her eyes away from her old friend.

"I understand, I have a certain diplomat to yell at anyway," Alec said, with no humor in his voice, turning towards the door.

"Hey Alec? He's going to be okay."

Alec turned around to face the blue warlock, nodding before leaving, closing the door behind him and putting his face in his hands. The thought of Magnus, the love of his life. The best thing that had ever happened to him, gone? Magnus was endgame for Alec. He could never fall in love with anyone else. Nothing like what he had with Magnus. The smartest, funniest, most powerful and, for the record, most attractive man he had ever met. Just eating Chinese takeout on the the floor of their apartment made Alec happier than he had ever thought possible.

With the sadness suddenly came the anger. At that jackass who broke the law and hurt his warlock. He started looking, room after room, for Aldertree, when he heard a familiar voice behind him.

"Alec? How is he? Magnus, I mean." Clary said, playing with her hair nervously.

"Uh, I don't know. Catarina said the magic she was using to heal him was too powerful for me to be around. She kicked me out. She said he should be okay. But, it was probably only to help me feel better." Alec's voice was shaking so much it took a little work to understand what he was saying.

"Magnus has helped me in so many ways, with my Mom, Jace, Simon, Luke, and pretty much everyone in my life. I will do anything to save him, Alec. I know how much you two love each other. It's kind of amazing, really." Clary said, looking into Alec's eyes, a small smile on her face.

"Thanks, Clary." Alec said back, trying to smile, but it only came out as barely a smirk.

"Clary, Alec. Come tell Mom and Dad what happened" Jace said, coming up behind Alec and placing a hand on his shoulder. Alec and Jace made eye contact, reading eachother in a way only parabatai could. Clary nodded at her boyfriend and followed the two boys out, looking towards Magnus' room with a worried glance.


End file.
